Distinct tissue-niche localization and function of synovial tissue myeloid DC subsets in health, and in active and remission Rheumatoid Arthritis

Lucy MacDonald^1.2# and Aziza Elmesmari^1.2# and Domenico Somma^1.2# and Jack Frew^1.2#, Clara Di Mario³, Roopa Madhu^4,5,6, Audrey Paoletti², Theodoros Simakou^1,2, Olympia Hardy^1,2, Barbara Tolusso³, Denise Campobasso³, Simone Perniola^3,7, Marco Gessi⁸, Maria Rita Gigante⁹, Luca Petricca⁹, Dario Bruno^1,3,7, Roberta Benvenuto⁸, John D. Isaacs^1,10,11, Andrew Filby¹², David McDonald¹², Jasmine P. X. Sim^1,10, Kevin Wei⁴, Maria Antonietta D’Agostino⁹, Neal L. Millar^1,2, Simon Milling^1,2, Charles McSharry², Elisa Gremese^1,3,7, Karen Affleck¹³, Kenneth F. Baker^1,10,11, Iain B. McInnes^1,2, Thomas D. Otto^1,2, Ilya Korsunsky^4,5,6, Stefano Alivernini^1,2,3,9 and Mariola Kurowska-Stolarska^1,2

1 Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), Glasgow, Birmingham, Newcastle, and Oxford, United Kingdom. 2 School of Infection & Immunity, University of Glasgow, United Kingdom, 3 Immunology Research Core Facility, Gemelli Science and Technology Park, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy. 4 Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA 5 Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA 6 Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA 7 Division of Clinical Immunology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy. 8 Institute of Pathology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy. 9 Division of Rheumatology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy. 10 Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom 11 Musculoskeletal Unit, Newcastle-upon-Tyne Hospitals, Newcastle upon Tyne, United Kingdom 12 Flow Cytometry Core Facility, Newcastle University, Newcastle upon Tyne, United Kingdom 13 Respiratory and Immunology Research Unit, GSK, Stevenage, United Kingdom

Equally contributing first^# and last^@ authors

*Corresponding authors: Stefano Alivernini: stefano.alivernini@unicatt.it Mariola Kurowska-Stolarska: Mariola.Kurowska-Stolarska@glasgow.ac.uk

This repository contains notebooks with code for the analysis of CosMx single cell spatial transcriptomics of synovial tissue from active RA and RA in sustained remission. These data are used for the localization of distinct myeloid DC and CD4 T cell populations in synovial tissue. These analyses include cell segmentation, coarse cell type annotation and reference annotation of subclusters using scRNAseq, niche identification and analysis of cell type colocalization.